Bio-intermediates for use in the chemical synthesis of polyketides

Abstract

The present invention relates to compounds made by a subset of modules from one or more polyketide synthase (“PKS”) genes that are used as starting material in the chemical synthesis of novel molecules, particularly naturally occurring polyketides or derivatives thereof. The biologically derived intermediates (“bio-intermediates”) generally represent particularly difficult compounds to synthesize using traditional chemical approaches due to one or more stereocenters. In one aspect of the invention, an intermediate in the synthesis of epothilone is provided that feeds into the synthetic protocol of Danishefsky and co-workers. In another aspect of the invention, intermediates in the synthesis of discodermolide are provided that feed into the synthetic protocol of Smith and co-workers. By taking advantage of the inherent stereochemical specificity of biological processes, the syntheses of key intermediates and thus the overall syntheses of compounds like epothilone and discodermolide are greatly simplified.

What is claimed is:  
     
         1 . A method for making a naturally-occurring polyketide comprising 
 fermenting a host cell containing an expression vector,    said vector comprising a recombinant gene encoding a polyketide synthase,    said synthase comprising modules from at least two different naturally-occurring polyketide synthases, wherein at least one of the naturally-occurring polyketide synthases does not naturally produce said polyketide, and    optionally isolating said polyketide from the fermentation medium.    
     
     
         2 . The method of  claim 1 , wherein the polyketide is an epothilone analog or a discodermolide analog.  
     
     
         3 . A method for making a first compound useful in synthesizing a second compound, wherein 
 said second compound contains four or more chiral centers, and    said first compound contains two or more chiral centers,    said method comprising expressing in a recombinant host cell a recombinant, non-naturally occurring polyketide synthase that produces said first compound.    
     
     
         4 . The method of  claim 3 , wherein the first compound contains at least 3 chiral centers, and the second compound contains at least 5 chiral centers.  
     
     
         5 . The method of  claim 3 , wherein the second compound contains at least 10 chiral centers.  
     
     
         6 . The method of  claim 3 , wherein the recombinant, non-naturally occurring PKS is either a portion of a naturally occurring PKS gene or is composed of portions of two or more naturally occurring PKS genes.  
     
     
         7 . The method of  claim 3 , wherein the second compound is an epothilone analog or a discodermolide analog.  
     
     
         8 . The method of  claim 3 , wherein said first compound is selected from the group consisting of:  
       
         
           
           
               
               
           
         
       
     
     
         9 . The method of  claim 3 , wherein said first compound is selected from the group consisting of 14-chloro-14-desmethyl-6-deoxyerythronolide B and 14-desmethyl-6-deoxy-14-(phenylthio)erythronolide B.  
     
     
         10 . The method of  claim 3 , wherein said first compound is selected from the group consisting of: 14-chloro-14-desmethyl-6-deoxy-8-hydroxyerythronolide B and 14-desmethyl-6-deoxy-8-hydroxy-14-(phenylthio)erythronolide B.  
     
     
         11 . A compound of the formula:  
       
         
           
           
               
               
           
         
       
       wherein 
 R 0  is C1-C8 alkyl, C1-C8 alkenyl, C1-C8 alkynyl, aryl, 2-phenylethyl, 2-(3-hydroxyphenyl)ethyl, or a group of the formula  
                     
 wherein R 1  and R 2  are each independently hydrogen, hydroxyl, or a hydroxyl protecting group; and X is O, NH, or N-alkyl;  
 R 3  is hydrogen, C 1 -C 10  alkyl or aryl;  
 R 4 , R 5 , R 6 , and R 7  are each hydrogen, or R 4  and R 5  together form a double bond and R 6  and R 7  together form a double bond; and  
 Y is hydroxyl, amino, —OC(═O)NH 2  or —NHC(═O)NH 2 , with the proviso that when R 3  is hydrogen or C 1 -C 6  alkyl that: (i) at least one of R 1  and R 2 is not hydroxyl, or (ii) R 4 , R 5 , R 6 , and R 7  are each hydrogen, or (iii) X is nitrogen, or (iv) Y is hydroxyl, amino, or —NHC(═O)NH 2 , or (v) any combination of (i) through (iv).  
 
     
     
         12 . The compound of  claim 11  that is:  
       
         
           
           
               
               
           
         
       
       wherein 
 R 1  and R 2  are each independently hydrogen, hydroxyl, or a hydroxyl protecting group;  
 R 3  is hydrogen, C 1 C 10  alkyl or aryl;  
 R 4 , R 5 , R 6 , and R 7  are each hydrogen, or R 4  and R 5  together form a double bond and R 6  and R 7  together form a double bond; and,  
 Y is hydroxyl, amino, —OC(═O)NH 2  or —NHC(═O)NH 2 .  
 
     
     
         13 . The compound of  claim 11  that is:  
       
         
           
           
               
               
           
         
       
       wherein 
 R 1  and R 2  are each independently hydrogen, hydroxyl, or a hydroxyl protecting group;  
 R 4 , R 5 , R 6 , and R 7  are each hydrogen, or R 4  and R 5  together form a double bond and R 6  and R 7  together form a double bond; and,  
 Y is hydroxyl, amino, —OC(═O)NH 2  or —NHC(═O)NH 2 , provided at least one of R 1  and R 2  is not hydroxyl.  
 
     
     
         14 . The compound of  claim 11  that is:  
       
         
           
           
               
               
           
         
       
       wherein 
 R 1  and R 2  are each independently hydrogen, hydroxyl, or a hydroxyl protecting group;  
 R 3  is hydrogen, C 1 -C 10  alkyl or aryl; and,  
 X is oxygen or nitrogen.  
 
     
     
         15 . The compounds of  claim 11  that are selected from the group consisting of:  
       
         
           
           
               
               
           
         
       
     
     
         16 . The compounds of  claim 11  that are selected from the group consisting of: